As discussed in the previous Ralsei's pronouns thread, these parentheticals were added to make the circumstances surrounding the they/them clear to the reader (for some specific posts, see 5774/71 and 5774/72; the specifier was supported by others in 5774/90, 5774/91, and 5774/94).
Regarding the consistency aspect, I don't think that anyone had objections to adding parenthetical specifiers to other characters referred to with multiple pronouns—it's just that it isn't a high priority, and no one has gotten around to doing it.
This dialogue has been brought up again and again and again, enough that there's now an editor note that explicitly states that it should not be added. Consensus is that "Character A uses they/them for Character B as an indication of Character A's unfamiliarity with Character B" is a common pattern in Deltarune's dialogue (e.g., Undyne for Alphys, Lancer for Noelle, Toriel for Susie), and that those should not be used as pronoun references.